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Applying Advanced In Vitro Culturing Technology to Study the Human Gut Microbiota
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Using culture 'omics to explore the microbial structure and function in an equid in vitro digestion model.

Simon Daniels1, Susan Martin2, Pat Harris3

  • 1Royal Agricultural University, Stroud Road, Cirencester, UK. simon.daniels@rau.ac.uk.

Scientific Reports
|December 1, 2025
PubMed
Summary

The equine in vitro gas production system (GPS) shows similar end-point metabolic profiles to donor feces but favors rumen microbes over equine gut bacteria, indicating potential functional redundancy.

Keywords:
Culture ‘omicsEquineGas productionMetabonomeMicrobiomeSustainability

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Area of Science:

  • Equine nutrition and microbiology
  • In vitro fermentation systems
  • Ruminant vs. Equid digestive physiology

Background:

  • The in vitro gas production system (GPS) is established for ruminant feedstuff analysis.
  • Adaptation of the GPS for equine research requires characterization of its microbial and metabolic behavior.
  • Understanding equine gut microbiome dynamics is crucial for optimizing nutrition.

Purpose of the Study:

  • To characterize the bacterial community and metabolome of equine fecal inoculum within the GPS.
  • To compare the microbial and metabolic profiles in the GPS with donor equine feces.
  • To assess the suitability of the GPS for equine nutritional studies.

Main Methods:

  • Six Welsh ponies on identical diets served as fecal donors.
  • Gas production was measured over 156 hours.
  • Bacterial community profiling (16S rRNA sequencing) and metabolomics (1H NMR) were performed on fecal and inoculum samples.
  • Viability PCR (PMAxx) assessed microbial viability.

Main Results:

  • Significant alterations in bacterial community profile and metabolic phenotype were observed over time in the GPS.
  • A transient system dysbiosis occurred at 8 hours.
  • End-point metabolic profiles in the GPS resembled donor feces, but fiber-degrading bacteria aligned more with rumen than equine literature.
  • The GPS accurately estimated dry matter digestibility.

Conclusions:

  • The equine GPS provides a similar end-point metabolic profile to donor feces and estimates digestibility accurately.
  • The system may favor rumen-associated microbes or exhibit functional redundancy compared to the native equine gut microbiome.
  • Further research is needed to fully validate the GPS for equine applications.